Measuring the Radius of Gyration and Intrinsic Flexibility of Viral Proteins in Buffer Solution Using Small-Angle X-ray Scattering

Abstract

Measuring structural features of proteins dispersed in buffer solution, in contrast to crystal form, is indispensable in understanding morphological characteristics of the biomolecule in a native environment. We report on the structure and apparent viscosity of unfolded α and β variants of SARS-CoV-2 spike proteins dispersed in buffer solutions. The radius of gyration of the β variant is found to be larger than that of the α variant, while the ab initio computation of one of the possible particle-like bodies is consistent with the small-angle X-ray scattering (SAXS) profiles resembling a conformation similar to the three-dimensional structure of the folded state of the corresponding α and β spike variant. However, a smaller radius of gyration with respect to the predicted folded state of 2.4 and 2.7 is observed for both α and β variants, respectively. Our work complements the structural characterization of spike proteins using cryo-electron microscopy techniques. The measurement/analysis discussed here might be useful for quick and cost-effective evaluation of several protein structures, let alone mutated viral proteins, which is useful for drug discovery/development applications.

An overview of descriptors to capture protein properties – Tools and perspectives in the context of QSAR modeling

“…Similarly, protein properties may be averaged and represented through convex hulls [72] or equivalent spheres that share a certain feature with the protein of interest. Accordingly, the radii of such spheres are descriptors too: for example, the hydrodynamic radius (also called the Stokes radius, equivalent to diffusion properties, [73] ) or the radius of gyration (equivalent to the moment of inertia, [74] , [75] ), which can be used to predict polymer-induced precipitation and/or diffusion in porous media as well as potential sites of molecular interactions [76] , [77] , [78] , [79] . Recently, models have been developed that correlate the hydrodynamic radius and radius of gyration for unstructured proteins [80] .…”

Sensing Dynamically Evolved Short‐Range Nanomechanical Forces in Fast‐Mutating Single Viral Spike Proteins

“…Some structural differences between the spike proteins characterized using small‐angle X‐ray scattering are also available in our recently published work. [ 47 ] Additionally, we would also like to mention that the behavior of virus and infectivity are complex and cannot be entirely explained by the properties of a single protein.…”

Computational formulation study of insulin on biodegradable polymers

“…An ensemble's radius of gyration distance in molecular dynamics trajectory can be used to predict elemental level compatibility packing of a bio-formulation. 38 In a varying thermodynamic simulation environment, a protein's radius of gyration (RG) is calculated as the sum of its principal moments. Thus, A radius of gyration is the distance between a rotation point and the system's overall potential energy.…”